Microbiome Data Visualization

Do you know how to read .qza file?

## Reading and exploring Artifacts (.qza)
SVs <- read_qza(file = "data/feature_table.qza", tmp = "data/tmpdir", rm = TRUE)

SVs$data[1:4,1:4]

otu_table(q2_ps)[1:4,1:4]

## Reading metadata
read_q2metadata("data/sample_metadata.tsv")[1:5, 1:5]

read_tsv("data/sample_metadata.tsv", comment = "#q2:types", show_col_types = FALSE)[1:5, 1:5] %>% 
  rename(SampleID="#SampleID")

## Reading taxonomy
taxonomy<-read_qza("data/taxonomy.qza")
head(taxonomy$data)

## Parse tidy taxonomy only
taxonomy<-parse_taxonomy(taxonomy$data)
head(taxonomy)


Citation

Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.


References

[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4


Appendix

Project main tree

.
├── LICENSE
├── PCoA.pdf
├── README.md
├── Rplots.pdf
├── Shannon_by_person.pdf
├── VennDiagram.2023-04-05_01-21-26.log
├── VennDiagram.2023-04-05_01-23-15.log
├── config
│   ├── config.yml
│   ├── pbs
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   ├── samples.tsv
│   ├── slurm
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   └── units.tsv
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── feature_table.qza
│   ├── metadata.csv
│   ├── rooted_tree.qza
│   ├── sample_metadata.tsv
│   ├── shannon.csv
│   ├── shannon_vector.qza
│   ├── taxonomy.qza
│   └── tmpdir
├── figures
│   ├── shannon_by_time.pdf
│   ├── shannon_by_time.png
│   ├── shannon_by_time.svg
│   ├── venn_metadata_shannon.pdf
│   ├── venn_metadata_shannon.png
│   └── venn_metadata_shannon.svg
├── images
│   ├── bioinformatics.png
│   ├── bkgd.png
│   ├── cgoods.png
│   ├── ml.png
│   └── rulegraph.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── report.html
├── requirement.txt
├── results
│   └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   ├── environment.yml
    │   ├── mothur.yml
    │   └── qiime220232.yml
    ├── report
    │   ├── barplot.rst
    │   ├── boxplots.rst
    │   ├── hcluster.rst
    │   ├── heatmaps.rst
    │   ├── nmds.rst
    │   ├── pcaordi.rst
    │   ├── pcoaordi.rst
    │   ├── sample_venn.rst
    │   ├── scatter.rst
    │   ├── shannon_div.rst
    │   └── workflow.rst
    ├── rules
    │   ├── qiime2_viz.smk
    │   ├── render_index.smk
    │   ├── rmd_report.smk
    │   └── rules_dag.smk
    └── scripts
        ├── README.md
        ├── common.R
        ├── import_qiime2_data.R
        ├── plot_line_point_errorbar.R
        ├── plot_venn_metadata_shannon.R
        ├── qiime2R.R
        ├── qiime2_phyloseq_object.R
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        └── tree.sh

15 directories, 75 files



Troubleshooting of FAQs

  1. Question
      2. Answer
  2. Question
      3. Answer